Download MendeleyCrystal structure of putative O-methyltransferase from Bacillus halodurans
Ramagopal, U.A., Patskovsky, Y.V., Almo, S.C.To be published.
2GPY
Crystal structure of putative O-methyltransferase from Bacillus halodurans
- PDB DOI: https://doi.org/10.2210/pdb2GPY/pdb
- Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
- Organism(s): Halalkalibacterium halodurans C-125
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2006-04-18 Released: 2006-06-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.248
- R-Value Work: 0.206
- R-Value Observed: 0.206
wwPDB Validation 3D Report Full Report
This is version 1.6 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| O-methyltransferase | 233 | Halalkalibacterium halodurans C-125 | Mutation(s): 8 |  | |
UniProt | |||||
Find proteins for Q9KDE1 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KDE1 Go to UniProtKB: Q9KDE1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9KDE1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | G [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.248
- R-Value Work: 0.206
- R-Value Observed: 0.206
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.567 | α = 90 |
| b = 62.807 | β = 90 |
| c = 137.746 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
| SHELXD | phasing |
| SHELXE | model building |
Entry History
Deposition Data
- Released Date: 2006-06-06 Deposition Author(s): Ramagopal, U.A., Patskovsky, Y.V., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2006-06-06
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2018-01-24
Changes: Structure summary - Version 1.5: 2018-01-31
Changes: Database references - Version 1.6: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
